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comparison snpSift_annotate.xml @ 16:f0e87bdad733 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 9d2052269bfbca81a5f9cd10c3153e611358a329
author iuc
date Tue, 24 Oct 2017 07:27:22 -0400
parents 8bd645802765
children ede8954f5c82
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15:8bd645802765 16:f0e87bdad733
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 SnpSift annotate 13 SnpSift -Xmx8G annotate
14 #if $annotate.id == 'id': 14 #if $annotate.id == 'id':
15 -id 15 -id
16 #elif str($annotate.info_ids).strip() != '': 16 #elif str($annotate.info_ids).strip() != '':
17 -info "$annotate.info_ids" 17 -info "$annotate.info_ids"
18 #end if 18 #end if
19 -q '$dbSnp' '$input' > '$output' 19 -q '$dbSnp' '$input' > '$output'
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> 22 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
23 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 23 <param name="dbSnp" type="data" format="vcf" label="VCF File with ID field annotated (e.g. dbSNP.vcf)"
24 help="The ID field for a variant in input will be assigned from a matching variant in this file."/> 24 help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
25 <conditional name="annotate"> 25 <conditional name="annotate">
26 <param name="id" type="select" label="Fields to annotate"> 26 <param name="id" type="select" label="Fields to annotate">
27 <option value="id">Only annotate ID field (no INFO fields will be added)</option> 27 <option value="id">Only annotate ID field (no INFO fields will be added)</option>
28 <option value="info">Add also INFO fields</option> 28 <option value="info">Add also INFO fields</option>